Position racks in the middle and lower third of the oven; preheat to 350 degrees F. Make the crust: Wrap the outside (bottom and side) of a 9-inch springform pan with foil. Coat the inside of the pan with cooking spray and line the bottom with parchment paper. Pulse the graham crackers, butter, sugar and salt in a food processor until fine moist crumbs form, about 1 minute. Press evenly into the bottom and 1/4 inch up the side of the prepared pan. Bake until set, about 15 minutes; transfer to a rack and let cool completely.
Make the topping: Line 2 baking sheets with foil. Spread the coconut on one and the pecans on the other. Bake, stirring the coconut once or twice, until the coconut and pecans are toasted, 12 to 15 minutes; let cool. Pulse the pecans in the food processer until coarsely chopped; transfer to a small bowl. Combine the butter, egg yolks, sugar, evaporated milk, vanilla and salt in a large saucepan. Bring to a simmer over medium heat and cook, stirring constantly, until the mixture reduces and caramelizes slightly, about 10 minutes. Stir in the chopped pecans and 1 1/2 cups coconut (reserve the remaining coconut for topping). Set aside to cool.
Make the cheesecake: Fill a roasting pan halfway with water and set on the lower oven rack. Put the chocolate in a microwave-safe bowl and microwave in 30-second intervals, stirring after each, until melted; let cool to lukewarm. Wipe out the food processor; add the cream cheese, sugar, eggs, cocoa powder and salt and pulse until smooth, about 2 minutes, scraping down the sides. Add the melted chocolate, sour cream and vanilla; pulse until combined.
Transfer about half of the batter to the prepared crust; smooth with a spatula. Spoon about two-thirds of the topping evenly over the batter. Top with the remaining batter; smooth the top. Set on the middle oven rack (directly over the pan of water) and bake until set around the edge but the center still jiggles slightly, 1 hour to 1 hour 15 minutes. Transfer to a rack and let cool to room temperature, then cover and refrigerate until cold and set, at least 8 hours or overnight.
Run a thin knife around the edge of the cheesecake and remove the springform ring. Microwave the remaining topping to soften, about 30 seconds (stir in 1 to 2 tablespoons water to loosen, if necessary). Spread on top of the cheesecake; top with the reserved coconut.